The 'Dot Fail' message means the base game cannot communicate with the Dotmation screen/controller.
Does the Dotmation display show anything (Williams Logo, Call Attendant, etc)?
If no, then likely the top power supply is bad (99% probability) or not connected (seeing that it's been in storage, don't know if things were disconnected before hand, but it's a long shot). Power supplies for the bottom and top are unobtainium now, but there is a tutorial made sticky at the top of this thread explaining how to make your own power supply from a basic ATX one. That would be your best bet.
If yes, then there a communication problem between the bottom slot and the topbox, but it could still be the power supply. Check all connections, especially the serial cable running from the controller board up top to the backplane on the lower part. Check all EPROMs on the controller board (should be 2 or 3 of them) to make sure they are installed properly.